pdb_extract - Tutorial

Tutorial for processing a structure solved by X-ray crystallography

The pdb_extract online tool extracts essential details from each step of your structure determination process in preparation for PDB deposition. Refinement statistics, for the most part, will be extracted from the header of your coordinate file. However, if it does not list specific statistics, the LOG files you provide within pdb_extract should supply these extra values. Such information is essential to include in today's PDB entries.

By providing the necessary files and information, you will receive two files in return: one mmCIF file with coordinate and refinement statistics (pdb_extract_coord_#.cif), and the other contains your structure factors (pdb_extract_sf_#.cif). The two files can be used as input for Validation and deposition to ADIT or ADITBeta.

Step 1: Make sure that the X-ray option is selected at http://pdb-extract.rcsb.org/.

Step 2: Upload your fully refined coordinate file into the box provided.

Step 2: Select the file format.

• Select PDB if the coordinate file is in PDB format.
• Select mmCIF if the coordinate file is in mmCIF format.

Step 3: Click the run button to get two frames in the next section.

• The two frames in the next section work independently. The upper frame is used to obtain all the structure factors used for structure refinement and the all the structure factors used for protein phasing, if you have them.

Step 4: Extract structure factors from the upper frame.

• Upload the file name of the structure factor  used for final refinement.
• Select the data type and the program names used for refinement.
• Click the RUN button in the bottom of the upper frame to get the structure factor in the next page.
• Save the mmCIF file in your local computer.

Step 5: Extract the key details about the structure from the lower frame.
This frame is used to extract key detail information from structure determination steps: protein phasing, molecular replacement, density modification, and final structure refinement.

• Upload the output file names exported from each crystallographic application step.
• Select the program names that export.
• Select the file format.
• Modify the chemical sequence in the molecular entity group, if necessary.
• Click the RUN button in the bottom of the lower frame
• Processing takes approximately 6 minutes, perhaps longer if your files are very large
• Save the mmCIF files (pdb_extract_coord_#.cif and pdb_extract_sf_#.cif) on your local computer

Step 6: Upload these two mmCIF files to ADIT or ADITBeta! for data submission.

Note: if you need help for each entry, please click the help button for the entry.

Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.